Modulation of the translocation of peptides through nanopores by the application of an AC electric field

Stefureac, Radu I.; Kachayev, Anton; Lee, Jeremy S.

doi:10.1039/c2cc17015a

Cited by 22 publications

(27 citation statements)

References 32 publications

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“…This result does not necessarily imply that the N‐terminal peptide was folded or aggregated, as its net charge is + 4, and, therefore, it will not be electrophoretically driven through the pore. It can, however, give rise to bumping events, owing to diffusion‐driven interactions with the pore . Surprisingly, on addition of Cu(II) (Fig.…”

Section: Resultsmentioning

confidence: 99%

Cu(II) and dopamine bind to α‐synuclein and cause large conformational changes

et al. 2014

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a-Synuclein (AS) is an intrinsically disordered protein that can misfold and aggregate to form Lewy bodies in dopaminergic neurons, a classic hallmark of Parkinson's disease. The binding of Cu(II) and dopamine to AS was evaluated by nanopore analysis with a-hemolysin. In the absence of Cu(II), wild-type AS (1 lM) readily translocated through the pore with a blockade current of À 85 pA, but mostly bumping events were observed in the presence of 25 lM Cu(II). A binding site in the N-terminus was confirmed, because Cu(II) had no effect on the event profile of a peptide consisting of the C-terminal 96-140 residues. In the presence of dopamine (25 lM), the translocation events at À 85 pA shifted to À 80 pA, which also represents translocation events, because the event time decreases with increasing voltage. Events at À 80 pA were also observed for the mutant A30P AS in the presence of dopamine. Event profiles for an N-terminal 1-60-residue peptide and a C-terminal 96-140-residue peptide were both altered in the presence of 25 lM dopamine. In contrast, dopamine had little effect on the CD spectrum of AS, and a single binding site with a K a of 3.5 9 10 3 M À1 was estimated by isothermal titration calorimetry. Thus, dopamine can interact with both the N-terminus and the C-terminus. Two-dimensional NMR spectroscopy of AS in the presence of dopamine showed that there were significant changes in the spectra in all regions of the protein. According to these findings, a model is presented in which dopamine induces folding between the N-terminus and C-terminus of AS. Partially folding conformations such as this may represent important intermediates in the misfolding of AS that leads to fibrillization.

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Section: Resultsmentioning

confidence: 99%

Cu(II) and dopamine bind to α‐synuclein and cause large conformational changes

et al. 2014

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“…On the experimental side, it has been shown that the translocation of DNA through a nanochannel can be modulated by dynamically changing the cross-section of an elastomeric nanochannel device by applying mechanical stress [48][49][50][51][52]. Time-dependent driving force are also used in the translocation process [53][54][55][56][57][58].…”

Section: Introductionmentioning

confidence: 99%

Polymer translocation through nano-pores: influence of pore and polymer deformation

2018

Preprint

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We have simulated polymer translocation across the a α-hemolysin nano-pore via a coarse grained computational model for both the polymer and the pore. We simulate the translocation process by allowing the protein cross a free-energy barrier from a metastable state, in the presence of thermal fluctuations. The deformation in the channel, which we model by making the radius of pore change from large to small size, can be originated by the random and non-random (systematic) cellular environment, drive out the polymer out of equilibrium during the transport dynamics. We expect that in more realistic conditions, effects originating on the translocation phenomena due to the deformability of the nano-pore can either decrease or increase the transport time of biomolecule passing through the channel. Deformation in channel can occurred because the structure of αhemolysin channel is not completely immobile, hence a small pore deformation can be occurred during translocation process. We also discuss the effects of polymer deformation on the translocation process, which we achieve by varying the value of the empirical and dihedral potential constants. We investigate the dynamic and thermodynamical properties of the translocation process by revealing the statistics of translocation time as a function of the pulling inward force acting along the axis of the pore under the influence of small and large pore. We observed that a pore with small size can speed down the polymer translocation process, especially at the limit of small pulling force. A drastic increase in translocation time at the limit of low force for small pore clearly illustrate the strong interaction between the transport polymer and pore. Our results can be of fundamental importance for those experiments on DNA-RNA sorting and sequencing and drug delivery mechanism for anti-cancer therapy.

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“…Since the size of fluid reservoirs is usually much larger than that of the nanopore, the local electric field within the nanopore is significantly higher than that in the fluid reservoir, resulting in slow particle motion within the fluid reservoir and high translocation velocity inside the nanopore. One of the major challenges in the nanopore-based technique is that DNA nanoparticles translocate through the nanopore too fast to be accurately detected [5,6,[17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36]. Although one can reduce the voltage bias applied across the nanopore to reduce the electric field inside the nanopore and consequently slow down the DNA translocation, lower voltage bias will simultaneously reduce the capture rate of the nanopore and the magnitude of the current change, leading to lower throughput and read-out accuracy.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, a relatively high voltage bias is typically applied across the nanopore in the nanoporebased DNA sequencing applications. To now, several methods have been proposed to slow down the DNA translocation through the nanopore to achieve higher read-out accuracy [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36]. They include increasing the solvent viscosity to increase the viscous drag force on the particle, lowering the fluid temperature to increase the fluid viscosity, adjusting salt concentration and/or salt type to modify the charge property of the nanopore by chemical functionalization of the nanopore or by an ionic field effect transistor, imposing a salt concentration gradient, utilizing optical tweezers, and conducting nanopores [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36].…”

Section: Introductionmentioning

confidence: 99%

Slowing down DNA translocation through a nanopore by lowering fluid temperature

et al. 2012

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In the next-generation nanopore-based DNA sequencing technique, the DNA nanoparticles are electrophoretically driven through a nanopore by an external electric field, and the ionic current through the nanopore is simultaneously altered and recorded during the DNA translocation process. The change in the ionic current through the nanopore as the DNA molecule passes through the nanopore represents a direct reading of the DNA sequence. Due to the large mismatch of the cross-sectional areas of the nanopore and the microfluidic reservoirs, the electric field inside the nanopore is significantly higher than that in the fluid reservoirs. This results in high-speed DNA translocation through the nanopore and consequently low read-out accuracy on the DNA sequences. Slowing down DNA translocation through the nanopore thus is one of the challenges in the nanopore-based DNA sequencing technique. Slowing down DNA translocation by lowering the fluid temperature is theoretically investigated for the first time using a continuum model, composed of the coupled Poisson-Nernst-Planck equations for the ionic mass transport and the Navier-Stokes equations for the hydrodynamic field. The results qualitatively agree with the existing experimental results. Lowering the fluid temperature from 25 to 0°C reduces the translocation speed by a magnitude of about 6.21 to 2.50 mm/sK (i.e. 49.82 to 49.71%) for the salt concentration at 200 and 2000 mM, respectively, improving the read-out accuracy considerably. As the fluid temperature decreases, the magnitude of the ionic current signal decreases (increases) when the salt concentration is high (sufficiently low).

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Modulation of the translocation of peptides through nanopores by the application of an AC electric field

Cited by 22 publications

References 32 publications

Cu(II) and dopamine bind to α‐synuclein and cause large conformational changes

Cu(II) and dopamine bind to α‐synuclein and cause large conformational changes

Polymer translocation through nano-pores: influence of pore and polymer deformation

Slowing down DNA translocation through a nanopore by lowering fluid temperature

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